dc.contributor.author | Dahlen, Oda | |
dc.contributor.author | van Erp, Titus Sebastiaan | |
dc.date.accessioned | 2018-03-09T12:10:53Z | |
dc.date.available | 2018-03-09T12:10:53Z | |
dc.date.created | 2015-08-18T12:58:51Z | |
dc.date.issued | 2015 | |
dc.identifier.citation | Journal of Chemical Physics. 2015, 142, 235101. | nb_NO |
dc.identifier.issn | 0021-9606 | |
dc.identifier.uri | http://hdl.handle.net/11250/2489801 | |
dc.description.abstract | Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones. | nb_NO |
dc.language.iso | eng | nb_NO |
dc.publisher | AIP Publishing | nb_NO |
dc.title | Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison | nb_NO |
dc.type | Journal article | nb_NO |
dc.type | Peer reviewed | nb_NO |
dc.description.version | publishedVersion | nb_NO |
dc.source.pagenumber | 9 | nb_NO |
dc.source.volume | 142 | nb_NO |
dc.source.journal | Journal of Chemical Physics | nb_NO |
dc.source.issue | 23 | nb_NO |
dc.identifier.doi | 10.1063/1.4922519 | |
dc.identifier.cristin | 1258587 | |
dc.relation.project | Norges forskningsråd: 237423 | nb_NO |
dc.relation.project | Norges forskningsråd: 209337 | nb_NO |
dc.description.localcode | © 2015 AIP Publishing LLC.Published by AIP Publishing. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.4922519 | nb_NO |
cristin.unitcode | 194,66,25,0 | |
cristin.unitname | Institutt for kjemi | |
cristin.ispublished | true | |
cristin.fulltext | preprint | |
cristin.qualitycode | 1 | |